Systems and methods for simulating gas flow dynamics of a real hydrogen fuel cell system using a computer, wherein the real hydrogen fuel cell system includes a gas container volume network having gas container volumes interconnected by gas transport lines. The method includes defining volume element and flow channel classes, defining a plurality of volume instances and a plurality of flow channel instances, for each flow channel instance, creating a first interconnection representation that defines a source container volume and a destination container volume for the flow channel instance, wherein the first interconnection representation mimics a portion of the gas container volume network of the real hydrogen fuel cell system, and simulating, using the first interconnection representation, a thermodynamic state for each of the volume instances, the thermodynamic state representing thermodynamic parameter(s) in each container volume of the gas container volume network of the real hydrogen fuel cell system.